In most countries, genomic evaluations are obtained from within-breed analyses. New Zealand (NZ) is an exception that has been doing genomic evaluations using a multi-breed reference population, including purebred and crossbred individuals, since 2007. This paper summarizes across-breed genomic prediction experiences in NZ. A number of areas are discussed including, breed stratification found in the SNP data, the prediction of breed proportions from SNPs, methods for building a multi-breed genomic relationship matrix (GRM) and the accuracy of across-breed genomic prediction from different across breed GRMs.
In the NZ population, accounting for the population structure in the GRMs had little effect on the validation accuracies and inflation measures from genomic selection analyses. It is suggested that prediction models that utilize breed-specific haplotype blocks based on high density SNP chips, along with a large training population, may improve genomic prediction in multi-breed populations.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Genetic Improvement Programs: Selection using molecular information, , 066, 2014
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